Download Oct 23, 2006 Handout

Oct 23, 2006 Handout
Answers to Student Questions
1. What happens when a base pair gets deleted?
a. If it is in a non-coding region, usually nothing. If it is in a coding region it
will cause a frameshift: because codons are made of three nucleotides,
deleting one base pair disrupts the “reading frame” or division of the
sequence into threes. Frameshifts occur if the number of base pairs
inserted or deleted is NOT a multiple of three (if three basepairs are
inserted or deleted it will add or delete an amino acid but the reading
frame will stay the same). Frameshift mutations are usually highly
disruptive and cause proteins to be non-functional.
2. Do all genes have only 2 alleles?
a. No. This is known as multiple allelism. Most genes have tens of alleles
present in the population. For an example we have discussed in class,
blood type in humans has 3 alleles.
3. Do outcomes of certain genotypes sometimes depend on a combination of other
preset genotypes?
a. By outcomes, if you mean phenotypes, the answer is yes. Some traits are
due to a combination of genes and genotypes. For example, eye color.
Eye color is not only dependent on the expression of multiple eye color
genes, but how dark or light the colors are depends on the amount of
melanin or pigment you have. For more on eye color (including banded
eye patterns and how is one eye brown and one eye green) read:
www.answers.com/topic/eye-color
4. Does co-dominance only work for blood types?
a. No. Example: pigment colors in orchids
5. Did Mendel know about co-dominance and incomplete dominance?
a. He seems to have known about incomplete dominance (with flowering
time). Some people list the “Principle of Incomplete Dominance” as one
of his main principles of discovery, but it’s not commonly attributed to
him.
Sequencing
Why do we need to sequence DNA?
The Sanger Method/Chain Termination Method 1977
1. Four reaction tubes:
From:
http://openwetware.org/images/thumb/b/be/Be109dideoxynucleotide.jpg/500pxBe109dideoxynucleotide.jpg
2.
From http://www.zerobio.com/sanger1.jpg
Dye Terminator Method
Mito Lab – PCR visualization by gel electrophoresis
Ladder
172 160 166 163 167 177 173
Ladder
500bp-
Chem E 355
Aut 06
182 159 164 175 170 168 171
500bp-
Ladder
161 162
500bp-
Ladder
500bp-
181 178 176 180 177
Ladder
500bp-
169 190 174
10-11-06
ChmE355/599
Transcription?
Z
O
O
O
O
P
P
P
P
Y
A
Low Glucose
High Lactose
O
High Glucose
Low Lactose
Z
Y
A
Z
Y
A
Low Glucose
Low Lactose
Z
Y
A
High Glucose
High Lactose
O
O
O
ChmE355/599
HOMEWORK DUE MON 10-30-06
Regulation
The trp operon. A group of genes whose enzymes synthesize the amino acid, tryptophan
are clustered together in the “trp operon.” These genes are transcribed when tryptophan
levels are low in the cell, i.e., when more tryptophan is needed. They are not transcribed
when tryptophan levels are high.
1.Based on the example of the lac operon, how do you think the trp operon might be
designed? (Hint: tryptophan is used continuously used by the cell so would the cell likely
have the operon continuously “turned on” or “turned off?”).
2. In class we’ve discussed how transcription can be controlled by transcription factors
(activators and repressors). Now think about what other potential control points exist.
Use the following example. In response to an environmental change, the bacterium
Escherichia coli alters the concentration of a particular protein (let’s call this hypothetical
protein, Protein X) over the course of a couple of hours. Which of the following are
reasonable (theoretically plausible) mechanisms by which the cell could change its
concentration of Protein X without affecting the concentrations of other proteins.
Specifically, could the cell…
A. Alter the sequence of the gene encoding for Protein X?
B. Alter the concentration of RNA polymerase in the cell?
C. Alter the concentration of nucleotides (NTPs) in the cell?
D. Alter RNA polymerase’s access to the promoter of the gene encoding/coding for
Protein X?
E. Alter RNA polymerase’s ability to move forward along the gene coding for Protein
X?
F. Alter the rate at which the mRNA coding for Protein X is degraded?
G. Alter the concentration of ribosomes in the cell?
H. Alter the ribosomes’ access to the ribosome binding site of the mRNA coding for
Protein X?
I. Alter the concentration of tRNA in the cell?
J. Alter the rate at which protein P is degraded?
3. In terms of energy and materials, what do you think would be the most “economical”
way for the cell to decrease the concentration of Protein X? Why?
4. What would be the quickest way to decrease the concentration of protein P? Why?